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		<title>Peak detection - Chromatogram builder</title>
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<h1>Chromatogram builder</h1>

<p style="color: red">
<b>
Starting with MZmine 2.39, this module is considered deprecated and will be removed in future MZmine versions. 
Please use the ADAP Chromatogram Builder, which is much faster and generates better results.
Contact the developers if you have any questions or concerns. 
</b>
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<h2>Description</h2>

<p>
The Chromatogram builder takes mass lists generated for each MS scan (see Mass detection) and builds a chromatogram for each mass that can be detected continuously over the scans.
Later, these chromatograms may be deconvoluted into individual peaks by the Deconvolution module.
</p>

<p>
This algorithm works by maintaining a pool of chromatograms spanning over consecutive scans. 
Only MS level 1 scans are considered for building the chromatograms.
For each processed scan, a mass list must be available (see Mass detection for details).
The mass list is processed in the 
order of decreasing intensity and each ion is connected to the appropriate chromatogram according to
the m/z tolerance parameter. 
When no matching chromatogram is found, a new chromatogram is created with the ioin's m/z value and added to the pool.
When a chromatogram is finished (no m/z peak is found to be connected to), its length (time span) and intensity (height) are checked according to user-specified minimal values.
Those chromatograms which fit the required parameters are added to the final peak list.
</p>

<h4>Method parameters</h4>
<dl>

<dt>Mass list name</dt>
<dd>Choose a name of the mass lists to be used for building chromatograms. The mass lists must be previously generated for each MS scan by the Mass detector module.</dd>

<dt>Min time span</dt>
<dd>Minimum time span over which the same ion must be observed in order to be recognized as a chromatogram. 
	The optimal value depends on the chromatography system setup. 
	The best way to set this parameter is by studying the raw data and determining what is the typical time span of chromatographic peaks.</dd>

<dt>Min height</dt>
<dd>Minimum intensity of the highest data point in the chromatogram. If chromatogram height is below this level, it is discarded.</dd> 

<dt>m/z tolerance</dt>
<dd>Maximum m/z difference of data points in consecutive scans in order to be connected to the same chromatogram.</dd> 

<dt>Suffix</dt>
<dd>The resulting chromatogram will be named <i>file name + suffix</i></dd> 

</dl>

<p>
The resulting chromatograms can be opened in the peak list table visualizer using a double-click:<br>
<img src="chromatograms.png" border="1">
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